rCST treatments preserved lung integrity and prevented long-term lung damage. BALB/c mice (n = 4 mice/group) were infected i.n. with NDM-1 K. pneumoniae (1.82 × 108 CFU/mouse) and then treated with an i.n. dose of rCST9/rCSTC (50 pg of each). The lungs were harvested at 24 h and 72 h p.i. A parallel group of mice were infected and treated i.n./i.p. or i.p. with rCST9/rCSTC as described herein, and then lungs were harvested at 5 and 10 days p.i. Serial sections of the lung were analyzed for histology (magnification, ×40) and apoptosis by using the TUNEL assay with DAPI to stain cell nuclei. (A) The i.n. administration of rCST9/rCSTC to infected mice markedly diminished immune cell infiltration into the lungs and edema at 24 h and 72 h p.i. compared to the high cellularity and signs of hemorrhaging and edema in the lungs of untreated infected mice. Further, lungs from mice treated with our two optimal rCST9/rCSTC treatments, obtained at 5 and 10 days p.i., showed prevention of long-term lung damage and resolution of inflammation. (B) Histopathological scoring of the lungs (0, no significant changes; 1, slight damage; 2, mild to moderate damage; 3, moderate to severe damage; and 4, severe damage) for three categories. The results showed that cystatin treatments significantly decreased lung damage compared to that at corresponding time points for untreated infected mice. Lungs from mice receiving rCSTs at 3 days p.i. and lungs collected from survivors at 5 and 10 days p.i. had mild to no damage, in contrast to the lungs of untreated infected mice (*, P < 0.05; **, P < 0.01). The scoring results are expressed as SQS (means and SEM). (C) Likewise, lungs from the same rCST-treated and infected groups showed markedly fewer apoptotic cells at 24 and 72 h p.i. All images are representative of the analysis of 4 to 6 sections per mouse.